19-44825957-T-G

Position:

• chr19-44825957-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.28 in 152,112 control chromosomes in the GnomAD database, including 6,585 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.28 (6585 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.40

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.359 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.280 AC: 42606 AN: 151994 Hom.: 6578 Cov.: 32

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.349

Gnomad AMR AF: 0.367

Gnomad ASJ AF: 0.349

Gnomad EAS AF: 0.166

Gnomad SAS AF: 0.221

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.325

Gnomad OTH AF: 0.290

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.280 AC: 42637 AN: 152112 Hom.: 6585 Cov.: 32 AF XY: 0.285 AC XY: 21160 AN XY: 74344

Gnomad4 AFR AF: 0.161

Gnomad4 AMR AF: 0.367

Gnomad4 ASJ AF: 0.349

Gnomad4 EAS AF: 0.167

Gnomad4 SAS AF: 0.221

Gnomad4 FIN AF: 0.386

Gnomad4 NFE AF: 0.325

Gnomad4 OTH AF: 0.286

Alfa AF: 0.320 Hom.: 16830

Bravo AF: 0.279

Asia WGS AF: 0.199 AC: 694 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.59
DANN	Benign	0.23

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs10402271; hg19: chr19-45329214;